[MMTK] dcd_to_nc : IOError: Database entry Atoms/ not found
jak at biogeo.uw.edu.pl
Fri Aug 1 08:29:29 UTC 2008
Seems that your problem is not dcd-related.
>> File "/usr/bin/dcd_to_nc", line 110, in <module>
And the important fragments fom dcd_to_nc script are:
16 usage = """Usage: dcd_to_nc [options] pdb_file dcd_file nc_file
18 pdb_file and dcd_file must describe the same system.
109 conf = PDBConfiguration(pdb_file)
It means that the problem occurs while reading pdb file.
You also have:
>> raise IOError("Database entry %s/%s not found" % (directory,
>> IOError: Database entry Atoms/ not found
Which means that for some reason it is looking for an atom that has space
(' ') as a symbol, which obviously it can not find.
Check your pdb file. Make sure it has well formatted atom names in correct
columns. Please note that atom field is 4 characters long and must have
spaces in right place. For example you should have ' C ' or and not '
C' or ' C ' or 'C '. See Notes on atom naming in
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